Inter-simple sequence repeats (ISSR) were used as markers to assess genetic diversity and population structure in two plant species, Empetrum nigrum (black crowberry) and Festuca richardsonii (arctic fescue), colonizing the volcanic island Surtsey since 1993 and 1973, respectively. The two species first appeared at the same site on the island, i.e. in the seagull colony. Based on the ISSR analysis, the species differed significantly in their genetic profiles. Although both species were found to be similar in terms of gene diversity, E. nigrum showed a relatively low level of polymorphism at the subpopulation level, whereas F. richardsonii was highly genetic structured. The shrub species retained its coarse genetic structure at subpopulation level, accompanied by a high gene flow and panmixis. As the species is still in its first generation on Surtsey, this structure may indicate a common source of genepool among the immigrants. On the other hand, the grass species, which established on the island much earlier and has since expanded rapidly into dense turfs, was found to be differentiated at the subpopulation level, revealing in some cases signs of genetic bottleneck linked with the founder effect.